Added all specifications for creating OM and EM

TODO: Clean it up the specifying OM and EM and work on the example.
Completed Establishing OM and EM in vignette.

It would be great if someone could check my work.
Subsequently I think Cole is the best person to look at the figures for the example.
The figures did not load in the vignette.pdf, and I am not sure why.
Merge branch 'edit_kfj' of github.com:seananderson/ss3sim into edit_kfj
Make minor vignette edits before merging to master
Merge branch 'edit_kfj' into master

Conflicts:
	vignettes/ss3sim-vignette.Rnw